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Online supplemental material Table S1 Field trial characteristics Location Foulum Aarslev Region in Denmark Central Jutland Funen Coordinates 09 o 34 E. 56 o 30 N 10 o 27 E. 55 o 18 N Plot size (m 2 ) 216 125 Soil type Loamy sand Sandy loam Clay (%) 9 13 Silt (%) 13 15 Sand (%) 74 70 ph (in 0.01 M CaCl 2 ) a 5.6 6.2 P (mg/100 g soil) a 4.4 2.8 K (mg/100 g soil) a 12 13 Mg (mg/100 g soil) a 4.2 4.4 a Mean for plough layer soil samples taken in March across all plots in the growing seasons 2006-2007 and 2007-2008 [1]

Table S2 Mean temperature and precipitation for different periods of the growing seasons 2006-2007 and 2007-2008 at the 2 locations Location Period Temperature ( C) Precipitation (mm) 2006-07 2007-08 2006-07 2007-08 Foulum a Oct-Mar 6.2 4.4 447 325 Apr-Jun 11.8 11.1 123 100 Jul-Aug 15.6 16.4 144 190 Aarslev b Apr-Jun 12.6 11.7 228 107 Jul-Aug 16.7 17.1 180 179 Sep-Oct 11.0 11.2 93 140 a Foulum, The Faculty of Science and Technology, Aarhus University, Denmark. b Aarslev, The Faculty of Science and Technology, Aarhus University, Denmark.

Table S3 Sowing and harvest time and irrigation for the growing seasons 2006-2007 and 2007-2008 at the 2 locations Crop Sowing date Harvest date Irrigation (mm) 2006-07 2007-08 2006-07 2008-09 2006-07 2008-09 Barley a 12 Apr 07 22 Apr 08 07 Aug 07 18 Aug 08 25 94 Faba bean a 12 Apr 07 22 Apr 08 28 Aug 07 01 Sep 08 25 94 Potato a 24 Apr 07 05 May 08 04 Sep 07 17 Sep 08 25 94 Wheat a 25 Sep 06 24 Sep 07 07 Aug 07 18 Aug 08 25 94 Rape seed a 18 Aug 06 22 Aug 07 19 Jul 07 29 Jul 08 - - White cabbage b 2 Apr 07 2 Apr 08 31 Oct 07 20 Oct 08 15 140 Oat b 12 Apr 07 15 Apr 08 8 Aug 07 15 Aug 08 8 - Carrot b 23 May 07 30 May 08 2 Oct 07 6 Oct 08 30 108 Onion b 21 Mar 07 4 Mar 08 27 Aug 07 18 Aug 08 30 140 a Location: Foulum, The Faculty of Science and Technology, Aarhus University, Denmark. b Location: Aarslev, The Faculty of Science and Technology, Aarhus University, Denmark.

Table S4 Fertilizer application rate in the 3 different growth systems a in the growing seasons 2006-2007 and 2007-2008 at the 2 locations Crop C OA OB N/P/K (Kg ha -1 ) b N/P/K (Kg ha -1 ) c N/P/K (Kg ha -1 ) d,e 2006-07 2007-08 2006-07 2008-09 2006-07 2008-09 Barley f 130/20/95 130/20/95 55/10/70 55/10/65 0/0/50 0/0/40 Faba bean f 0/25/125 0/25/125 0/0/75 0/0/60 0/0/75 0/0/60 Potato f 140/30/205 140/30/150 115/25/125 110/20/160 0/0/100 5/0/80 Wheat f 165/20/105 165/20/105 105/20/130 110/25/110 0/0/75 0/0/60 Rape seed f 190/25/90 185/25/85 95/25/135 95/25/90 0/0/90 0/0/90 White cabbage g 310/45/145 310/45/145 240/20/80 210/15/85 145/10/50 125/10/50 Oat g 90/15/45 90/15/45 50/5/15 40/5/15 - - Carrot g 120/20/60 120/20/60 60/5/20 50/5/20 - - Onion g 170/80/65 170/80/65 115/10/40 100/5/40 70/5/25 65/5/25 a C: conventional growth system; OA: organic growth system with animal manure; and OB: organic growth system with cover crops. b Applied as inorganic fertiliser. c Applied as animal manure. K was supplemented as vinasse for all crops from Foulum. d K was applied as vinasse for all crops from Foulum. e Animal manure was also applied to white cabbage and onion in the OB system. f Location: Foulum, The Faculty of Science and Technology, Aarhus University, Denmark. g Location: Aarslev, The Faculty of Science and Technology, Aarhus University, Denmark.

Table S5 Pesticides used in the conventional system in the growing seasons 2006-2007 and 2007-2008 at the 2 locations Crop 2006-07 2007-08 Barley a OxitrilCM. Amistar. Unix OxitrilCM. Amistar. Unix Faba bean a Cypermethrin Cypermethrin. Pirimor G Potato a Fenix. Titus. SweDane Contact. Shirlan. DithaneNT. Cypermethrin. Reglone Wheat a Starane. Express. Opus. ProlineEC250. Amistar. Cypermethrin Fenix. Titus. SweDane Contact. Shirlan. DithaneNT. Cypermethrin. Reglone Starane. Express. Opus. ProlineEC250. Amistar. Cypermethrin Rape seed a Kerb 500SC. Matrigon. IT-Cypermethrin Command CS. Loncid. IT-Cypermethrin White cabbage b Dipel ES 1.5. Fastac 50. Pirimor Dipel ES 1.5. Fastac 50. Pirimor. Amistar Oat b Express ST. Starane 180S. MCPA 750. Stereo 312.5 EC. Amistar Express ST. Starane 180S. MCPA 750. Stereo 312.5 EC. Amistar Carrot b Afalon. glyphosate Afalon. Fenix. glyphosate. Amistar. Signum WG. Fastac 50 Onion b Stomp. Totril. Acrobat WG. Dithane NT Stomp. Totril. Fenix. Acrobat WG. Dithane NT. Signum WG. Fastac 50 a Location: Foulum, The Faculty of Science and Technology, Aarhus University, Denmark. b Location: Aarslev, The Faculty of Science and Technology, Aarhus University, Denmark.

Table S6 Harvest yields a for all crops in the 3 different growth systems b in the growing seasons 2006-2007 and 2007-2008 at the 2 locations Crop Season C P e OA P e OB P e P f Barley c 2006-07 4.75 ± 0 51 # 3.20 ± 0.08 $ 3.65 ± 0 07 $ 0.003 0.03 2007-08 5.48 ± 0 19 # 3.29 ± 0.5b $ 4.53 ± 0.02 & 0.02 Faba bean c 2006-07 2.26 ± 0.04 1.95 ± 0.17 2.11 ± 0.05 0.02 0.03 2007-08 3.57 ± 0.26 2.50 ± 1.01 3.45 ± 0.35 Potato c 2006-07 43.5 ± 3.75 # 0.02 29.3 ± 1.44 $ 0.03 27.2 ± 2.24 $ 0.02 2007-08 61.5 ± 0.55 # 46.4 ± 3.66 $ 38.9 ± 3.95 $ 0.01 Wheat c 2006-07 7.01 ± 0.33 # 0.02 3.58 ± 0.27 $ 0.04 1.81 ± 0.16 & 0.04 0.0006 2007-08 9.47 ± 0.39 # 5.03 ± 0.32 $ 2.75 ± 0.22 & 0.0005 White cabbage d 2006-07 83.2 ± 4.57 62.8 ± 1.41 68.1 ± 7.63 0.02 0.009 2007-08 106 ± 1.58 91.9 ± 3.58 91.3 ± 12.7 Oat d 2006-07 5.00 ± 0.03 # 0.007 4.62 ± 0.14 #$ 0.02 4.23 ± 0.28 $ 0.049 2007-08 3.06 ± 0.07 3.59 ± 0.13 3.84 ± 1.17 Carrot d 2006-07 95.9 ± 3.37 83.9 ± 7.56 90.5 ± 6.54 0.04 2007-08 108 ± 0.99 $& 102 ± 2.74 #& 94.5 ± 2.69 # 0.02 Onion d 2006-07 73.8 ± 0.26 # 0.02 47.5 ± 10.1 $ 50.3 ± 4.03 $ 0.04 2007-08 95.7 ± 3.80 # 64.0 ± 0.99 $ 61.7 ± 9.07 $ 0.02 a Values are means ± SD (n = 2) expressed as ton fresh weight/hectare.

b C: conventional growth system; OA: organic growth system with animal manure; and OB: organic growth system with cover crops. c Location: Foulum, The Faculty of Science and Technology, Aarhus University, Denmark. d Location: Aarslev, The Faculty of Science and Technology, Aarhus University, Denmark. e P-value for the effect of the growing season on the harvest yields of the crops from each growth system (Student s t-test). f P-value for the effect of growth system on the harvest yields of the crops. Values not sharing the common superscript within each row are different at given P-value (ANOVA). References 1. S. Husted, B. F. Mikkelsen, J. Jensen and N. E. Nielsen, Elemental fingerprint analysis of barley (Hordeum vulgare) using inductively coupled plasma mass spectrometry, isotope-ratio mass spectrometry, and multivariate statistics, Anal Bioanal Chem, 2004, 378(1), 171-182.